Hello Ahmed,

There are two options that could help you to design a probe for a target gene. 

First, depending on how conserved the gene is, try to design a probe to the area of the sequence that has the most differences between other genomes in that family. Sometimes, even 2 or 3 nt difference can be enough to significantly increase the melting temperature of the probe and the correct sequence. Either a molecular beacon or a taq man probe with a melt curve analysis could help you to determine how effective this method would be in your case. 

Second, if you are trying to find an area in the 3 or 5' untranslated region that is different between targets for identification of a desired sequence, you could try to determine the sequence yourself. Depending on your resources you could try to sequence the genome or use known sequences to generate primers that amplify portions of the UTR and sequence those to find a new target for your probe. 

Good luck with your probe!

Thank you so much Thomas